Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1hska2
CCHHHHHHHHHHHHHHHHHHCCC--CCCEECCCCCCCC--------------------------CCCHHHHHHHCCCCCCEECCEEECCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC--------CCCC

>P1;d1uxya2
---CCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCEECHHHHHHHHHHCCCCCEEECCCCCEEECHHHHHHHCCCCCCEECCEEECCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEECCEECCHHHHHC
PSA

>P1;d1hska2
a7997567856766876675205--7471348006609--------------------------b5612700560a02334380010064402100216b07a612250054037105653826073638379--------997a

>P1;d1uxya2
---66976677654866755315587261572006414155940980287269032563b982130201200340903025271000166301000538a069713360043013500740903060527165aa7457138306


Translating the sequences
***HHHHHHHHHHHHHHHHHCCC--CCCEE**CCCCC*--------------------------**CHHHHHHHCCCCCCEECCEEECCCCCC*EEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCC**--------***C
---**HHHHHHHHHHHHHHHCCC**CCCEEEECCCCCE**************************EECHHHHHHHCCCCCCEECCEEECCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE********HHHC

56194.tem
_________________________________
---HHHHHHHHHHHHHHHHHCCC--CCCEEEECCCCCE--------------------------EECHHHHHHHCCCCCCEECCEEECCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE--------HHHC




Structural block scores
0	2	-	3.0	P	  8.8  75.0

3	19	H	4.8	H	  6.5  6.2

20	22	C	5.0	H	  2.3  3.0

23	24	-	3.0	P	  75.0  6.5

25	27	C	5.0	H	  6.0  5.0

28	31	E	4.0	M	  4.0  3.8

32	36	C	5.0	H	  2.4  2.2

38	63	-	3.0	P	  75.0  4.8

64	65	E	3.0	P	  8.2  1.5

67	73	H	5.0	H	  3.0  1.4

74	79	C	5.0	H	  3.1  2.3

80	81	E	5.0	H	  3.5  3.5

82	83	C	5.0	H	  4.0  4.0

84	86	E	5.0	H	  0.3  0.0

87	92	C	5.0	H	  2.7  2.8

93	96	E	4.5	M	  0.8  1.2

97	101	C	5.0	H	  5.1  5.5

102	120	H	5.0	H	  3.4  2.9

121	130	C	5.0	H	  4.6  3.3

131	132	E	3.0	P	  8.0  5.5

133	140	-	3.0	P	  75.0  6.0

141	143	H	3.0	P	  8.3  3.7

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